


Pepper Potts, (Social) Scientist Supreme

by TardisIsTheOnlyWayToTravel



Category: Iron Man (Movies), Marvel (Comics), Marvel (Movies), Marvel Avengers Movie Universe, The Avengers (2012)
Genre: A.I.M., Banter, Crack, Ensemble Cast, Evil Scientists - Freeform, F/M, Humour, Pepper is a BAMF, Pepper is made of awesome, Ridiculousness, The Avengers - Freeform, idek, villain!Pepper, what is this i do not even, you're not supposed to flirt with the bad guys Tony
Language: English
Status: In-Progress
Published: 2013-03-05
Updated: 2013-06-22
Packaged: 2017-12-04 08:51:31
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 3
Words: 4,289
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/708871
Author URL: https://archiveofourown.org/users/TardisIsTheOnlyWayToTravel/pseuds/TardisIsTheOnlyWayToTravel
Summary: <blockquote class="userstuff">
              <p>When Pepper didn't get the P.A. job at Stark Industries, she applied for an administrative position at Advanced Idea Mechanics instead.</p><p>It didn't take her long to work her way to the top of the ladder through a combination of ruthless competence, people skills, and a good working knowledge of organisational psychology. Unfortunately, after Loki is dealt with, the Avengers decide to take care of A.I.M. next, which interferes with Pepper's well-laid plans.</p><p>To make it worse, Tony Stark - aka Iron Man, aka the most infuriating yet charming man Pepper has ever met - presents a problem all of his own. Not that Pepper's going to let him know that, of course.</p>
            </blockquote>





	1. Chapter 1

**Author's Note:**

> I'm trying to decide if I should rename this something like 'Pepper Potts, Criminal Mastermind.' LMK?
> 
> Also, this was inspired by a [prompt](http://avengerkink.livejournal.com/15292.html?thread=33012668#t33012668) on avengerkink, although it doesn't exactly match it.

**Pepper Potts, (Social) Scientist Supreme**

The man sitting at the desk opposite Pepper smiled at her. A slimeball, Pepper had already concluded, but one who kept his true nature under wraps until he was behind closed doors for fear of damaging his reputation.

“Well, Ms Potts,” Obadiah Stane said, interlocking his fingers and resting them on the desk. “Your qualifications and experience are impressive. In fact, you seem to be exactly what we want.”

Pepper’s hopes rose for a moment. Working at Stark Industries was said to be a challenge, and frankly everything she’d heard about Tony Stark said we was a horror to deal with, but Pepper was _good_ at what she did, the projected salary for the P.A. position was excellent, and to be honest Pepper was curious about whether Stark was really as brilliant everyone said he was behind the playboy veneer.

But before she could get too excited, Stane directed another greasy smile at her.

“Unfortunately, I’m sure you’re aware of Tony’s reputation,” Stane continued. “Women have always been his weakness. To be honest, you’re too pretty to make a productive assistant. While I’m sure you’re a complete professional,” and Stane’s voice was patently insincere, “Tony would spend all his time trying to seduce you. I’m sure you see the problem.” He gave her another one of those smiles.

_ Too pretty to make a productive assistant.  _ Pepper took a deep breath, and sent him a smile that sparkled with icy rage.

“Oh, I see the problem,” Pepper said calmly. “And I’d suggest that it’s with Stark Industries’ discriminatory hiring policies and attitude towards sexual harassment. If you’ll excuse me, my time is valuable, and you’ve wasted enough of it today.”

And Pepper stood, with a queen-like grace and composure that had take years to achieve, and walked out of the interview without another word.

* * *

Pepper was still seething as she went through the ads that the hiring agency had sent her. _Too pretty._ The nerve! The fact that that loathsome man had sat there and told her, _to her face_ , that while her qualifications were perfect she was _too pretty_ for the job, because Stark couldn’t keep it in his pants and Stane had clearly thought that she’d just… _give in_ to his advances, as though she were some – some _floozy_ who didn’t take her job seriously…

“I hope,” Pepper said savagely, as she found a promising job listing, “that someone screws that man over for everything he’s worth.”

* * *

Pepper’s next interview was for a senior administrative assistant job with the Board of Directors of a robotics company named the Adarco Corporation. While the corporation had a very well-organised website, talking about how the company was dedicated to progress and a brighter future (their mission statement was similarly impressive-but-vague) there was little in the way of actual _information_ about what Adarco produced. Pepper supposed that it was possible that that company had secretive military or private contracts that prevented their products from being disclosed to the public.

On paper, everything looked good, but Pepper’s first clue that something was up was the fact that every. Single. Person. she saw working for her prospective employer was dressed in a blinding shade of yellow. Pepper’s eyes were watering by the time she made it to the interview room.

She was greeted by an older woman in a pant suit of a slightly more sedate shade of yellow, who introduced herself as Irene Morgan, the Chairwoman of the Board of Directors. 

Pepper was asked about her qualifications – the fact that for her undergraduate degree she had minored in psychology (and taken a number of electives in organisational psychology) seemed to be a point in Pepper’s favour, as the Chairwoman said something approving about social science – and her extensive experience. There were also a number of probing questions about Pepper’s regard for internal policies (strong), her ability to keep company secrets (excellent), and her business ethics (ruthless).

At the end of the interview, the Chairwoman smiled, and offered Pepper a hand to shake.

“I think you’ll do very well here, Ms Potts. We always value intelligent, competent employees capable of dealing with our, if I’m honest, rather demanding administrative practices. Welcome to the company.”

Pepper shook the proffered hand, and gave her best professional smile in return.

“Thank you, I’m sure working here will be a positive experience. I have just one question, if you don’t mind. This might sound a little strange, but I couldn’t help noticing that everyone here seems to dress in yellow. Is that part of the mandatory dress code?”

Ms Morgan’s smile dimmed a little.

“Unfortunately, yes.”

“ I see.” Pepper didn’t let her smile slip even slightly, as she contemplated what wearing neon yellow would do to her complexion. Perhaps she would be permitted to wear something in the one shade of medium yellow that actually suited her? (As it turned out, the answer was yes, although finding a women’s suit in that colour turned out to be a Herculean task all of its own.) 

* * *

Pepper wasn’t stupid, so it didn’t take her long to work out that Adarco wasn’t exactly what it pretended to be. It took her two weeks, via clandestine research and the subtle interrogation of her co-workers, to discover that the robotics company was actually a front for a terrorist organisation named Advanced Ideas Mechanics (A.I.M.).

After uncovering as much as she could about A.I.M.’s activities, Pepper spent a lot of time thinking.

Most people assumed that because she was polite, and law-abiding, and believed in being nice to people unless they’d done something to deserve otherwise, that Pepper was the stereotypical ‘good person’ (not that the phrase had any real meaning, of course, as vaguely-defined and subjective as it was). But the truth was that Pepper was ruthless in pursuit of her aims, cunning, and had a moral system that had been variously described as ‘idiosyncratic’ and ‘flexible’, and which one particular individual had bluntly summed up as “ _reflecting whatever is you want to do at the time, Virginia Potts, because you’re a frigging social CHAMELEON_.” 

While that particular summation had been harsh and unfair, it was true that Pepper’s morals were somewhat variable depending on her situation and the moral values of the people around her. The question was, did working for A.I.M. conflict with those morals? 

While Pepper didn’t like the idea of a violent overthrow of the government – she disliked people being hurt unnecessarily, and the kind of sudden, dramatic regime-change most of the organisation seemed to have in mind would lead to inefficiency and chaos, which Pepper deplored – she found that when she thought about it, she agreed that the current global systems of government was in need of overhaul. There were too many despotic regimes, too much corruption even in the most democratic nations, and even sound principles of government were usually compromised by a lack of objectives-based focus and inability to see the big picture – the world was a complex system full of unpredictable variables linked by causal relationships, but how many politicians and government workers understood that? So no, Pepper was not opposed to changing the current systems of government _per se_ , although she believed that it should be possible to do so with less loss of order and productivity than A.I.M. seemed to have included in its planning. And of course, if you were going to change the world… well, technology was the obvious way to do it, as long as you didn’t fall into the same traps as the people you intended to replace.

Her moral quandary resolved, Pepper waited for a quiet moment to approach the Chairwoman of the Board.

“Is there something you wanted, Miss Potts?” Irene asked, looking up with the pleasant smile she usually reserved for the senior administrative assistants. It was clear that unlike some members of the Board of Directors, Irene was well-aware of the wisdom of staying on the good side of the people who organised your affairs.

No one’s career ever advanced by being shy and retiring, Pepper told herself, firmly quashing her nerves. Competence, assertiveness and initiative always won the day.

“I was wondering,” she asked politely, “if there was some way I could find out more about A.I.M.’s goals and objectives.”

Irene didn’t look remotely surprised. Instead, her smile widened.

“Talk to Mr Peters. I’m sure he could find you copies of the _real_ mission statement. It’s very informative.”

Pepper thanked her, and went to see the head of Administration.

* * *

It turned out that Irene hadn’t been kidding when she had said that the organisation could always use intelligent, capable people: as far as Pepper could discover, they had almost _none_.

Oh, to be sure, everyone was an expert in their field, and had usually honed their particular skills as much as was possible, but there was no comprehension of _anyone_ _else’s_ _skills_ , or their value, or the fact that everyone in A.I.M. was hired because their abilities or ideas were either necessary or highly desirable. Simply put, there was no _cohesion_ in the organisation as a whole, with different departments – sometimes even different individuals – trying to claim power and push forward with their own agendas, because they had no understanding of the importance of everyone else’s. It was disastrous, and it was one of the reasons, Pepper was sure, that none of A.I.M.’s more ambitious goals had yet succeeded, despite their resources and the amount of time that A.I.M. had been active.

It was time, Pepper decided, to further her education in organisational theory.

* * *

It was at about this time that Obadiah Stane was killed in a tragic accident, leaving Tony Stark the sole owner of Stark Industries. That evening Pepper bought a bottle of champagne to celebrate, while she paged through the report that detailed the true circumstances of the man’s death, which had been compiled by one of the intelligence agents that A.I.M. had planted in Stark Industries.

It was annoying that A.I.M would be losing their source of the more restricted Stark tech now that Stane was dead, but all the same, Pepper privately wished Tony Stark the best of luck.

* * *

While Irene was open to Pepper’s ideas – unlike most of the Board, who were all prominent scientists themselves, and didn’t hold other disciplinary streams in particularly high regard – it took a while for the other senior members of A.I.M. to accept them. After a while, however, they started to notice that the changes Pepper had suggested made the organisation more productive, and became a lot more willing to take notice of any policy suggestions Pepper made. Her progress through A.I.M.’s organisation hierarchy skyrocketed.

After six months, Irene officially notified the rest of the Board of Directors that she intended to retire, and to Pepper’s shock, nominated her as a possible successor. To Pepper’s even greater shock, the Board concurred, and Pepper became the newest member of the A.I.M.’s Board of Directors.

After that, it didn’t really take long before Pepper was made the Chairwoman of the Board, and given the official internal title of Scientist Supreme, after some discussion whether it was appropriate for someone who had only studied social science to be granted such a title. To be honest, although Pepper had never expected to become the head of a terrorist organisation, she privately admitted that she had never enjoyed herself more.

Then the Chitauri and Loki invaded, and everything changed.

 

 


	2. Chapter 2

**Notes for the Chapter:**

> So, seriously, this is just a silly thing I do occasionally, for fun. No kind of update schedule or proper plot, okay? That said, if you enjoy it, awesome.

**Chapter Two**

The Chitauri Invasion caused destruction and a loss of life which on a personal level, left Pepper appalled. From the perspective of the head of A.I.M., however, it was catastrophic. Half their plans were thrown into disarray, a significant number of their people were left dead – it was going to take time and effort to get things back on track.

That would have been bad enough. But after the Avengers had taken care of Loki, they decided to go after A.I.M. next. The first that Pepper knew of any of this was when their primary SHIELD mole failed to report in. Twelve hours later, one of A.I.M.’s secret bases was attacked. A.I.M. had several secret bases, and there was little of relative importance taking place at this particular base. Really, the main reason Pepper even cared was that she happened to be in it at the time.

As she made her escape via the secret tunnel reserved for senior personnel only, Pepper was pleased to note that all the evacuation drills appeared to have paid off, as A.I.M.’s employees fled the base in a hasty but organized manner by exiting through the series of secret escape routes that had been installed all over the base.

Pepper’s momentary sense of satisfaction didn’t last long after she emerged from the secret tunnel. There was a blur of red and gold, and Pepper screamed as she was snatched up by a pair of arms and thrown over a metallic shoulder before Iron Man took off again.

The world whizzed past at high speed and upside down, and Pepper wasn’t sure which bothered her more, the nausea she was experiencing or the indignity of her position.

“Put me down this instant!” Pepper yelled, pounding on Iron Man’s back with zero effect.

“Nope, I don’t think so,” an electronic voice responded cheerfully, barely audible over the rush of air around them.

“Then at least _slow down!_ ” Pepper howled. “Unless you want me to be sick all down the back of your armour!”

Iron Man seemed to think this was reasonable, because he slowed his speed until Pepper felt less like she was about to throw up. Pepper resigned herself to her current position for however long it took for Iron Man to reach wherever it was he was taking her. 

A moment later the ground came up to meet them as Iron Man landed. Pepper didn’t struggle – she was wearing a _short skirt_ , and this was mortifying enough as it was – as Iron Man swung her down to land on slightly unsteady feet.

“There you go. Anyone ever tell you you’ve got nice legs?”

Pepper glanced at the bright optics of the suit with a raised eyebrow.

“Really, Mr Stark?” she asked dryly. “You just caught me attempting to escape from A.I.M.’s secret base, and _that’s_ what you want to ask me?”

Iron Man shrugged.

“Well, I’ve had a good view of them for the last several minutes, they were kind of on my mind. Thanks for not screaming the entire time, by the way. It gets old.”

“ _Stark!_ ” someone yelled. “Stop flirting with the bad guys!”

Pepper reached up to pat her hair and check that it was all still in place. Thank God for industrial strength hairspray. She reached up, ostensibly to check her earrings, and dug her thumbnail into the groove on the back of her left earring to activate her personal distress beacon.

“Here’s another one for you, Coulson!” Iron Man called. “I caught her escaping out the V.I.P. tunnel!”

Several S.H.I.E.L.D. agents immediately moved forward to take Pepper into custody.

“Later, Lovely Legs,” said Iron Man, and blasted off into the sky.

Pepper demurely allowed herself to be searched, handcuffed, and led off to a S.H.I.E.L.D. van that would take her to a secure S.H.I.E.L.D. facility.

Five minutes into their journey, the van was attacked by plain-clothes A.I.M. agents who extracted Pepper and spirited her away to safety.

Ten minutes after that, the countdown Pepper had initiated before her escape hit zero and all of the explosives wired throughout the A.I.M. base went off, burying the entire base in rubble.

* * *

The base was an irritating loss, but not a serious one. The loss of their most well-placed S.H.I.E.L.D. mole, on the other hand, was a genuine setback. Pepper wasn’t pleased about it.

She was in the middle of a planning session with the rest of the Board when her phone went off. Pepper stared at the caller ID. It said that her mother was calling. Her mother _never_ called.

Pepper excused herself from the meeting, and went outside to take the call.

“Mom?”

“Pepper!” Her mother sounded worried. “Baby, is there something you want to tell me?”

Oh, lovely, Pepper hated this game. She wracked her brain to try and figure out what secret her mother might have discovered, but couldn’t think of anything.

“No?”

“Because that nice Tony Stark came around to the house yesterday and said he thought you might have got mixed up with terrorists and could be in all kinds of trouble!” Pepper froze. _No._ “He said you might be in danger, and asked us all these questions…”

Pepper bit her lip. That complete _bastard_. Despite her fury, Pepper couldn’t help but feel a certain grudging respect. It had clearly been masterfully done, too, because her mother sounded genuinely worried instead of offended that someone had implied that Pepper was less than perfect.

“Mom. Did you give him this number?”

Pepper made rapid calculations, kicking herself for not foreseeing this. Stark had probably found out everything he needed to know. Then there was her phone – it potentially meant GPS co-ordinates, access to moderately sensitive text messages… and considering that this was Tony Stark, it was likely that he was fully capable of retrieving all of it, especially since Pepper used the Stark Phone service.

“Of course,” Pepper’s mother replied, innocently puzzled, and Pepper smacked her forehead with her palm. _Damn._

“Okay, well, Mom? I’m going to be changing my phone number very soon, and I don’t want you to give the number to anyone else, okay? No matter what anyone tells you.”

“Pepper, what’s going on? What have you gotten yourself into?”

“I’m fine, Mom. I’ll ring you soon, but I’ve got to go.” Pepper hung up before her mother could say anything else.

She took a deep breath, centering herself. It was probably that everything and everyone in this building was now compromised. They certainly couldn’t afford to behave as thought it wasn’t.

With deep regret, Pepper thought of her penthouse apartment, no doubt swarming with S.H.I.E.L.D. agents. It was just as well that Pepper had moved all the important things out of her apartment straight after escaping SHIELD custody. There were a couple of pairs of Jimmy Choos and Manolo Blahniks she was going to miss, though. Another thing to blame Stark and S.H.I.E.L.D. for.

With a sigh, Pepper went to inform the rest of the Board that they were compromised, and needed to fix the situation.


	3. Chapter 3

**Notes for the Chapter:**

> I don't know if anyone caught it, but for like the first hour it was up, I accidentally had the wrong version of chapter two uploaded. So you might want to duck back and check that you're acquainted with the current version, which has one scene less (because that scene is going somewhere else).

**Chapter Three**

Pepper was in her office, reviewing the latest joint project proposal from the engineering and biological sciences department (a mind-control device disguised as a Bluetooth earpiece? really?) when her intercom chimed.

“Yes?”

“ _Scientist Supreme,_ ” the senior administrative assistant said. “ _Security have just apprehended an intruder. He was discovered in the air vents._ ”

Pepper’s brow furrowed at the news.

“I see. Have him brought up to my office. Thank you, Evangeline.”

Five minutes later a small squad of security men entered Pepper’s office, escorting a muscular man in an armless black vest with the S.H.I.EL.D. logo on it. Trailing behind them was a small pack of the mobile sentry robots that patrolled the air vents and maintenance areas. A couple of robots were dragging along a bow and a quiver full of arrows.

Pepper stared at the intruder. He looked rather the worse for wear. Pepper wondered exactly how many robots had swarmed him.

“Uh, hi?” Hawkeye offered. “So, the vents: _not_ the best entry point?”

“Not really, no,” Pepper agreed, still eyeing him consideringly. Then she leaned forward to look down at the sentry robots over the top of her desk.

“You did _very_ well,” she cooed warmly. For some reason the sentry robots were very sensitive to both praise and criticism. But they did their job, so Pepper was willing to go with it. “I’m very pleased. You can go back to your duties, now. Leave the bow and arrows.”

The robots chirped in happy acknowledgement and scuttled out, while Hawkeye stared at them.

“In addition to the weapons, he also had these, ma’am.” One of the security people held out one of the small soundproof boxes they used to store confiscated bugs and other communications technology.

Pepper opened the box to see a headset with an earpiece and microphone. Pepper swiped a tissue over the earpiece and fitted it into her ear.

“ _I fear that Hawkeye has been taken captive by the enemy,_ ” said a deep, ponderous voice. 

Pepper’s lips curved into a slight smile.

“Well,” she said into the microphone, “we can’t have people wandering through the air vents. You didn’t really think that the vents were unmonitored, did you?”

“ _Identify yourself!_ ” ordered a male voice. At the same time, a different voice – one Pepper recognised from TV broadcasts – demanded, “ _who the hell are you?_ ”

“My name is Virginia Potts, Mr Stark. I believe you paid my mother a visit.”

There was a momentary pause, then Stark responded.

“ _Ms Potts, we meet again. It’s Pepper, right? Your mom called you Pepper. How’s Hawkeye?_ ”

“More or less unharmed,” Pepper said lightly. “Although the air vent defences are surprisingly vicious.”

“ _I’ll keep that in mind_ ,” said Stark, his voice grim behind the casual facade. “ _I’m curious: is he likely to stay unharmed?_ ”

Pepper realised that she was enjoying herself.

“Well, that depends on the Avengers. Tell me, what exactly were you planning, sending Hawkeye into our air vents? Should I be planning for any more unexpected guests?”

“ _What, you object to a little company?_ ” Stark quipped.

“It helps if they use the front door,” Pepper answered, in the same tone. While she was talking, she opened the top drawer of her desk and pulled out her phone. It was an iPhone, unfortunately, rather than her previous, tremendously functional Stark Phone, but the iPhone didn’t use the Stark Phone communications network, which (hopefully) made it marginally more difficult for Stark to hack into.

_ Contingency 37B _ , Pepper texted her assistant. 

“ _I guess you’re not the spontaneous type who likes surprise visits,_ ” Stark conceded.

“I like my schedule,” Pepper agreed, writing out a set of instructions on her notepad. “And since you seem to have side-tracked this conversation, I reiterate: why exactly was there an Avenger crawling around in my air vents?”

The door to Pepper’s office opened, and a promising young man with interesting ideas about how to disable the major communications networks – David Welles, Pepper recalled – sidled in nervously, clutching his laptop. Pepper gestured wordlessly to the security staff for Hawkeye to be turned so that he was facing the wall. As soon as his nose was pressed to the paint Pepper held up her notepad so that Welles could read it.

Brightening, the young engineer nodded in comprehension and sat, and began typing at his laptop busily.

“ _Just a little reconnaissance, seeing what the neighbours are up to; you know,_ ” Stark replied breezily. “ _You’re not really that surprised, right? I mean, we did raid one of your other bases._ ”

Welles gave a triumphant grin and turned the laptop around so that Pepper could see the screen.

_ Are those their coordinates? _ Pepper mouthed. Welles nodded smugly. Pepper texted her assistant again.

“More annoyed than surprised,” Pepper told Stark. “Having the base raided dramatically decreases productivity.”

“ _Really? Fancy that. Listen, how about you put Hawkeye on? Not that I don’t trust you, or anything – although I seriously don’t – but it’d be nice to have some proof you’re telling the truth about him being unharmed._ ”

“I could do that,” Pepper said noncommittally. Her phone pinged, and she read the text message with satisfaction. “You do realise that your comm. units have a detectable frequency, right?” She paused, to give the Avengers a moment to put it together. “And that all of them are emitting a signal on that frequency? Which we have?”

“ _Shit_ ,” Stark said in realisation. Then, “ _Move! They’ve got our position! Everyone_ –”

There was a hiss of static, and the line went dead. Still smiling, Pepper removed the earpiece and microphone. Opening the top drawer of her desk again she pulled out a small metal cylinder.

“I want all the priority projects out of this base and all the data transferred to the backup servers within the next twenty minutes, and the base evacuated,” Pepper said calmly. “The process should already have begun. Anything that cannot be removed in that time is to be destroyed. I want nothing useful left behind for S.H.I.E.L.D. to find. Make sure that everyone follows procedure.” She stood up, and walked around her desk.

“What about this one?” one of the security people asked. Instead of responding, Pepper stepped forward to where Hawkeye still stood with his nose against the wall and swiftly pressed the cylinder she held to the side of his neck. There was a puff of displaced air, and a moment later Hawkeye slowly crumpled to the floor, twitching slightly.

“Leave him somewhere outside the blast zone. S.H.I.E.L.D. can find him later.”

“And his weapons?”

Pepper glanced at the bow and quiver of arrows, still on the floor where the robots had left them. She grinned slightly.

“Leave them with me.”


End file.
